Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate GFF558 Psest_0563 urea ABC transporter, ATP-binding protein UrtE
Query= uniprot:D8IUY7 (241 letters) >FitnessBrowser__psRCH2:GFF558 Length = 232 Score = 169 bits (427), Expect = 6e-47 Identities = 97/228 (42%), Positives = 143/228 (62%), Gaps = 6/228 (2%) Query: 5 ILKVQQLSVAYGGIQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASRVEGHI 64 +L+VQQL YGG ++G+ E GE+ L+G NG GKTT LK + G +PA EG + Sbjct: 1 MLQVQQLHQYYGGSHILRGLSFEAKVGEVTCLLGRNGVGKTTLLKCLMGLIPAK--EGAV 58 Query: 65 EYLGQPLKGKKSFELVKDKLAMVPEGRGVFTRMSIQENLLMGAYTSDDKGQIAADIDKW- 123 + G+P+ G K + V +A VP+GR +F R++++ENLLMG S + A ++ ++ Sbjct: 59 NWEGKPITGFKPHQRVHAGIAYVPQGREIFGRLTVEENLLMGL--SRFSAREAKEVPEFI 116 Query: 124 FAVFPRLKERAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPIMVEKIFEVI 183 + +FP LKE + G LSGG+QQ LA+ RAL S P+LL+LDEP+ G+ P ++++I VI Sbjct: 117 YELFPVLKEMKHRRGGDLSGGQQQQLAIGRALASKPRLLILDEPTEGIQPSVIKEIGAVI 176 Query: 184 RNVSAQG-ITILLVEQNAKLALEAAHRGYVMESGLITMQGQAQQMLDD 230 R ++A+G + ILLVEQ A E A + VM G I QG+ + M D Sbjct: 177 RKLAARGDMAILLVEQFYDFAAELADQYLVMSRGEIIQQGRGENMAAD 224 Lambda K H 0.317 0.134 0.365 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 154 Number of extensions: 10 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 241 Length of database: 232 Length adjustment: 23 Effective length of query: 218 Effective length of database: 209 Effective search space: 45562 Effective search space used: 45562 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory